Setup document

Let’s create your first R Markdown documents.

1. Open RStudio
2. Create a new R Markdown file. To do so, click on File -> New File -> R Markdown

Create R Markdown File

This should prompt a dialog that allows you to choose whether you want your output to be in html, pdf or word format. For now, we will go with html, but you can always change this later.

Output format

This will provide you with a template for an R Markdown document. In this file, you will be able to write code and text, and even import images in R Studio. Sounds pretty awesome, doesn’t it? Let’t chickly safe the file so that we don’t loose anything. Click on File - Save and give it a filename.

Knit

Now to really make things look pretty (aka compile the html document) we need to knit the file. In order to do so, simply click on knit on the top left.

Knit

Let’s get starting filling this document with some content, but first of all, we should get rid of all the template content provided. Make sure to keep the header, and the piece of code that set’s up the structure of the document, but delete everything below. You should just be left with this bit of the code:

---
title: "Intro to R Markdown"
output: html_document:
---

```{r setup, include=FALSE}
knitr::opts_chunk$set(echo = TRUE)
```

Headings

You can structure your reports by including headings and subsections. Headings are added by adding a # before your heading. Adding more # makes your heading a sub(or sub, or sub-sub-) heading.

## Heading 2
### Heading 3
#### Heading 4

Which should look like this:

Paragraphs

You create paragraphs by leaving an empty line between sentences. That is to say simply hitting enter won’t do the job, you actually need to leave an empty line.

This is your first sentence. 
This will NOT be a new paragraph. 

This however will be one!

Which looks like so:

This is your first sentence. This will NOT be a new paragraph.

This however will be one!

Give this a try with the text you have added before. Create some paragraphs and subsections.

Text formatting

Lastly, you can make text italic (*italic*) or bold (**bold**), and include inline code (`code`).

You can also include links [text](link), i.e. [Cambridge Neuroscience](https://www.neuroscience.cam.ac.uk) get’s you to Cambridge Neuroscience.

Code Blocks

The great thing about R Markdown is that you can add code directly into your report. This will allow you to add plots - and even show the code that produced it.

You can add codeblocks either by clicking on Code > Insert Chunk, or by adding the following directly:

```{r }

```

Give it a try. Let’s add some code to your report. We will use the basic R dataset iris. As a first step, we probably want to get an idea of what the data looks like. Go ahead and create a new code chunk Now in that code chunk, type:

head(iris)

If you now knit the file, you should see the head of the iris dataframe displayed:

##   Sepal.Length Sepal.Width Petal.Length Petal.Width Species
## 1          5.1         3.5          1.4         0.2  setosa
## 2          4.9         3.0          1.4         0.2  setosa
## 3          4.7         3.2          1.3         0.2  setosa
## 4          4.6         3.1          1.5         0.2  setosa
## 5          5.0         3.6          1.4         0.2  setosa
## 6          5.4         3.9          1.7         0.4  setosa

However, we also see the code you used to produce the table. If you just want to show your readers an overview of the dataframe, you won’t need to show the code. We can hide it, by adding the option echo=F to your code chunk like this:

```{r echo = F}

```

Tables

While the code above works well to demonstrate some options in R Markdown, the table that is output does not actually look too pretty. Let’s change that. The knitr::kable() function allows you to easily create pretty tables. Try out changing the above head(iris) to:

knitr::kable(
  head(iris), # This is the table we will plot
  booktabs = TRUE, # We determine the formatting style as 'booktabs'
  caption = 'A table that now looks much prettier.') # Here we are adding a caption 

Figure Options

Perfect. Let’s plot some data. Create a new code chunk and paste this code into it. Make sure you have the ggplot2 library installed. If you haven’t, install it first by typing install.packages('ggplot2') into the console.

library(ggplot2)
ggplot(iris, aes(x= Sepal.Length, color = Species, fill = Species, alpha = 0.4)) + 
  geom_density() + 
  theme_bw()

This should create a plot like this:

Don’t want people to see your code? Remember to add echo = F. Find the output too big? You can decide on the exact dimensions (in inches) by adding fig.width = 3, fig.height = 2. Alternatively, you could scale it to a percentage of the original dimensions using: out.width = '50%'. Lastly, decide how the figure should aligned using fig.align = 'center'. Go ahead and give some of these options a try.